Shalabh,
Also take a look at this:
http://www.bioperl.org/wiki/HOWTO:SearchIO#frame.28.29
Brian O.
On Jul 2, 2012, at 3:34 PM, Peter Cock wrote:
> On Mon, Jul 2, 2012 at 6:09 PM, shalabh sharma
> <shalabh.sharma7 at gmail.com> wrote:
>> Hi All,
>> I am just confused about the translation frames. I used bioperl to
>> parse a blastx report.
>> Reports shows that the frame used is -2 but when i translate the sequence
>> using EMBOSS or Some other program the frame is -1.
>> Am i doing something wrong here.
>> Possibly there are conflicting definitions of frames -1, -2, and -3 here
> (and that's leaving out the possibility of -0, -1 and -2 counting). Some
> will count from the first base (start for forward strand), others the last
> base (start of reverse strand). This can make comparing the output
> of different tools quite confusing.
>> Peter
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